Contacts of the helix formed by residues 452 - 470 (chain B) in PDB entry 2Y0N
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 452 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202B CYS* 3.3 20.7 - - - -
204B THR 3.9 13.5 - - - -
206B ILE* 3.3 16.9 - - - +
209B ILE* 3.9 0.9 - - - -
451B TYR* 1.3 75.4 - - - +
453B ALA* 1.3 65.6 + - - -
454B GLN* 3.2 4.9 + - - -
455B HIS* 3.3 4.7 + - - -
456B LEU 3.2 18.0 + - - -
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Residues in contact with ALA 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B THR 4.6 1.2 + - - -
209B ILE* 3.4 23.7 - - + +
452B GLY* 1.3 71.7 - - - -
454B GLN* 1.3 67.4 + - - +
456B LEU* 3.9 6.1 - - - +
457B LEU* 3.3 19.2 + - - +
491B LEU* 5.7 4.4 - - + +
498B PHE* 3.5 33.4 - - + +
499B PHE* 3.4 26.7 - - + -
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Residues in contact with GLN 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B GLN* 5.0 1.1 - - - +
184B LEU* 5.1 1.0 - - - +
187B ASP* 4.0 10.2 - - - +
198B VAL* 3.8 22.3 - - + +
202B CYS* 4.3 2.9 - - - -
452B GLY* 4.0 5.9 + - - -
453B ALA* 1.3 87.2 + - - +
455B HIS* 1.3 70.5 + - + +
457B LEU* 3.8 4.7 + - - +
458B ARG* 3.2 22.0 + - - +
498B PHE 4.1 16.6 + - - -
499B PHE* 4.1 19.0 - - + +
500B PRO* 4.4 6.3 + - - +
503B ALA* 3.4 28.3 - - - +
504B TYR* 3.2 34.3 - - + +
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Residues in contact with HIS 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B VAL* 3.6 34.8 - - + +
265B PHE* 3.7 29.1 - - + -
269B LEU* 4.0 11.2 - - + -
273B LEU* 4.3 2.9 - - + +
274B LEU* 4.5 3.5 - - + +
278B GLU* 3.0 11.7 + - - -
281B GLN* 5.6 2.2 + - - -
451B TYR* 3.3 39.1 - + + +
452B GLY 3.3 7.4 + - - +
454B GLN* 1.3 76.9 - - + +
456B LEU* 1.3 66.7 + - - +
457B LEU 3.1 2.2 - - - -
458B ARG* 3.0 58.5 + - + +
459B LEU 3.4 4.0 + - - -
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Residues in contact with LEU 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ILE* 3.8 30.5 - - + -
209B ILE* 4.1 21.8 - - + -
210B LEU* 4.4 5.4 - - + -
261B LEU* 4.3 18.2 - - + +
265B PHE* 3.8 13.7 - - + -
452B GLY 3.2 16.9 + - - +
453B ALA* 3.9 5.4 - - - +
454B GLN 3.5 0.2 - - - -
455B HIS* 1.3 75.1 - - - +
457B LEU* 1.3 63.5 + - - +
459B LEU* 3.2 25.7 - - + +
460B PHE* 3.3 24.9 - - + -
487B PHE* 3.8 25.6 - - + -
491B LEU* 5.0 6.5 - - + -
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Residues in contact with LEU 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B ILE* 5.2 3.4 - - + -
180B LEU* 3.8 31.6 - - + +
183B GLN* 4.0 12.8 - - + -
184B LEU* 3.8 34.5 - - + +
453B ALA 3.3 14.4 + - - +
454B GLN 3.9 5.4 - - - +
455B HIS 3.1 0.6 - - - -
456B LEU* 1.3 77.2 - - - +
458B ARG* 1.3 67.5 + - - +
460B PHE* 3.0 24.8 + - + +
461B VAL 3.9 1.7 + - - -
488B LEU* 4.1 25.4 - - + -
491B LEU* 4.4 9.2 - - + +
499B PHE* 4.0 21.5 - - + -
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Residues in contact with ARG 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B LEU* 4.1 9.4 - - + -
187B ASP* 2.5 43.1 + - - +
191B ILE* 3.5 11.9 - - - +
273B LEU* 3.2 30.4 + - + +
274B LEU* 4.6 0.2 - - - +
275B TYR* 3.7 10.6 - - - -
278B GLU* 2.6 39.3 + - - -
454B GLN 3.2 18.7 + - - +
455B HIS* 3.0 35.5 + - - +
457B LEU* 1.3 76.6 - - - +
459B LEU* 1.3 62.2 + - - +
461B VAL* 2.9 24.0 + - - +
462B LYS 3.6 1.0 + - - -
589F PHE* 3.5 42.9 - - + -
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Residues in contact with LEU 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261B LEU* 3.9 26.2 - - + +
264B THR* 4.3 8.1 - - + -
265B PHE* 4.2 27.1 - - + +
268B THR* 3.9 36.1 - - + +
273B LEU* 3.7 17.8 - - + +
455B HIS 3.4 2.4 + - - +
456B LEU* 3.2 19.2 + - + +
458B ARG* 1.3 78.6 - - - +
460B PHE* 1.3 55.5 + - + +
462B LYS* 3.0 3.3 + - + -
463B LEU* 2.8 52.3 + - + +
466B ILE* 4.4 6.7 - - + -
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Residues in contact with PHE 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B ILE* 4.5 15.4 - - + +
176B ILE* 4.3 15.0 - - + +
261B LEU* 3.6 26.0 - - + -
456B LEU* 3.3 22.9 - - + -
457B LEU* 3.0 18.2 + - + +
459B LEU* 1.3 76.0 - - + +
461B VAL* 1.3 60.5 + - - +
463B LEU* 4.1 16.8 - - + +
464B PRO* 3.7 13.3 - - - +
484B PHE* 3.9 31.9 - + + -
487B PHE* 3.4 40.4 - + - -
488B LEU* 3.9 35.2 - - + -
491B LEU* 4.9 0.9 - - + -
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Residues in contact with VAL 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B ILE* 3.8 12.1 - - + -
184B LEU* 3.8 28.9 - - + -
457B LEU 4.7 0.4 - - - +
458B ARG 2.9 12.6 + - - +
460B PHE* 1.3 80.2 - - - +
462B LYS* 1.3 66.6 + - + +
464B PRO* 3.5 15.1 - - - +
465B GLU* 4.2 3.5 - - - +
589F PHE* 3.9 23.8 - - + -
590F GLU 4.2 3.8 - - - +
591F LEU* 4.6 3.1 - - + -
592F PRO* 3.6 33.9 - - + +
593F TRP* 4.5 10.5 - - + -
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Residues in contact with LYS 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B VAL* 3.5 32.3 + - + +
273B LEU* 3.7 26.5 - - + -
458B ARG 3.6 0.4 + - - -
459B LEU* 3.0 7.1 + - + +
461B VAL* 1.3 79.5 - - + +
463B LEU* 1.3 65.8 + - - +
464B PRO* 3.3 0.9 - - - -
465B GLU* 3.2 50.7 + - + +
466B ILE* 3.4 20.7 + - + +
587F GLN* 3.0 38.8 + - - +
588F ASN 4.9 3.0 + - - -
589F PHE* 4.0 21.1 - - + +
590F GLU 4.8 8.8 + - - +
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Residues in contact with LEU 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B ILE* 3.7 14.1 - - + -
261B LEU* 4.8 5.2 - - + -
264B THR* 4.7 10.8 - - + -
459B LEU* 2.8 52.8 + - + +
460B PHE* 4.2 12.8 - - + +
462B LYS* 1.3 75.6 - - - +
464B PRO* 1.3 65.8 - - + +
466B ILE* 3.0 9.1 + - + +
467B LEU* 2.8 42.2 + - + +
484B PHE* 3.5 46.4 - - + -
577F PHE* 5.3 4.0 - - + -
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Residues in contact with PRO 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B ILE* 3.3 46.8 - - + +
174B ILE* 3.8 18.4 - - + +
460B PHE 3.7 10.3 - - - +
461B VAL* 3.5 17.5 - - - +
462B LYS 3.4 1.3 - - - -
463B LEU* 1.3 93.0 - - + +
465B GLU* 1.3 64.6 + - + +
467B LEU* 3.4 3.1 + - + +
468B GLY* 3.0 21.3 + - - -
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Residues in contact with GLU 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461B VAL 4.2 3.8 - - - +
462B LYS* 3.2 50.2 + - - +
464B PRO* 1.3 78.3 - - + +
466B ILE* 1.3 65.3 + - + +
468B GLY* 3.3 10.3 + - - -
469B LYS* 3.5 23.6 + - - +
584F LEU* 6.0 2.0 - - + -
587F GLN* 5.1 4.1 + - - +
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Residues in contact with ILE 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264B THR* 4.7 10.5 - - + -
267B TYR* 6.5 0.4 - - + -
268B THR* 4.1 22.7 - - + +
272B VAL* 4.9 0.4 - - + -
459B LEU* 4.4 6.5 - - + -
462B LYS* 3.5 26.5 - - + +
463B LEU* 3.0 10.2 + - + +
465B GLU* 1.3 75.8 - - + +
467B LEU* 1.3 59.4 + - + +
469B LYS* 3.0 24.7 + - - +
470B MET* 3.3 35.6 - - + +
581F LEU* 5.1 0.9 - - + -
582F PRO* 3.7 21.3 - - + +
584F LEU* 3.9 33.9 - - + -
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Residues in contact with LEU 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B ILE* 4.0 16.4 - - + +
174B ILE* 3.9 15.0 - - + -
463B LEU* 2.8 47.8 + - + +
464B PRO* 3.8 5.4 - - + +
466B ILE* 1.3 69.3 - - + +
468B GLY* 1.3 60.4 + - - +
470B MET* 2.8 38.3 - - + +
472B PHE* 3.5 36.4 + - + -
477B LEU* 5.0 2.0 - - + -
480B LEU* 4.0 13.0 - - + -
481B LEU* 4.4 10.3 - - + -
484B PHE* 3.9 9.6 - - + -
577F PHE* 4.4 11.9 - - + -
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Residues in contact with GLY 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B ILE* 4.0 11.8 - - - +
464B PRO 3.0 14.7 + - - -
465B GLU 3.3 5.6 + - - -
466B ILE 3.2 0.2 - - - -
467B LEU* 1.3 76.8 - - - +
469B LYS* 1.3 61.9 + - - +
470B MET 3.5 5.2 + - - +
471B SER* 4.6 3.3 + - - -
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Residues in contact with LYS 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465B GLU* 3.5 17.2 + - - +
466B ILE* 3.0 9.6 + - - +
468B GLY* 1.3 78.9 - - - +
470B MET* 1.3 57.2 + - - +
471B SER* 3.9 2.1 + - - -
582F PRO* 3.8 16.8 - - + -
583F LYS* 3.3 27.4 + - - +
584F LEU* 4.1 18.9 - - + +
585F ALA 5.6 0.6 - - - +
569H THR* 3.2 31.9 + - + +
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Residues in contact with MET 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264B THR* 5.3 2.2 - - + -
466B ILE* 3.3 44.0 - - + +
467B LEU* 2.8 35.1 - - + +
468B GLY 3.8 1.9 - - - +
469B LYS* 1.3 74.6 - - - +
471B SER* 1.3 60.1 + - - +
472B PHE* 3.0 32.1 + - + -
576F ALA 4.5 7.4 - - - +
577F PHE* 5.0 6.3 - - + -
579F ARG* 3.7 23.3 - - + +
580F PRO* 3.7 22.2 - - + +
581F LEU* 4.0 13.2 - - + -
582F PRO* 3.9 11.7 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il